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Introduction Reduced bone mineral density (BMD) is a well-recognised extraintestinal manifestation of coeliac disease (CD) and increases fracture risk. Identifying patients at risk at the time of diagnosis is essential to optimise management and prevent long-term skeletal complications.Methods We conducted a retrospective observational cohort study including 237 adult patients with biopsy-confirmed coeliac disease, selected from 344 patients followed between 1995 and 2025 in a tertiary referral centre. Bone mineral density was assessed at diagnosis using dual-energy X-ray absorptiometry and classified according to WHO criteria. Low BMD was defined as osteopenia (T-score −1 to −2.5) or osteoporosis (T-score ≤ −2.5). Clinical, endoscopic and histological variables were analysed. Factors associated with low BMD were assessed using univariate analysis followed by multivariable logistic regression.Results A total of 237 patients were included (median age 34 years, 76% female). Low BMD at diagnosis was identified in 74 patients (31.2%), including osteopenia in 59 (24.9%) and osteoporosis in 15 (6.3%). Low BMD was more frequent in women (35.9% vs 16.1%, p = 0.005) and in patients presenting with abdominal pain at diagnosis (44.7% vs 27.9%, p = 0.026). Histological severity strongly influenced bone density: 50.8% of patients with Marsh 3B/3C lesions had low BMD compared with 23.8% of those with less severe lesions (p < 0.001).In multivariable analysis (n = 183), Marsh 3B/3C histology (OR 2.50, 95% CI 1.24–5.02; p = 0.010) and severe villous atrophy (subtotal or total) (OR 2.89, 95% CI 1.03–8.12; p = 0.044) were independently associated with low BMD. Age and diagnostic delay were not associated with BMD. The multivariable model showed good discriminative ability (AUC = 0.70).Conclusions Low bone mineral density is frequent at the time of coeliac disease diagnosis. Severe histological involvement, particularly Marsh 3B/3C lesions and extensive villous atrophy, independently predicts low BMD. These findings support systematic bone density assessment at diagnosis, especially in patients with severe mucosal damage.